University of Oulu

Ponna, S. K., Myllykoski, M., & Kursula, P. (2018). Crystallographic home-source X-ray data for the atomic-resolution experimental phasing of the Shank3 SH3 domain structure from pseudomerohedrally twinned crystals. Data in Brief, 20, 1912–1916.

Crystallographic home-source X-ray data for theatomic-resolution experimental phasing of theShank3 SH3 domain structure frompseudomerohedrally twinned crystals

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Author: Ponna, Srinivas Kumar1; Myllykoski, Matti1; Kursula, Petri1,2
Organizations: 1Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
2Department of Biomedicine, University of Bergen, Norway
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 0.6 MB)
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Language: English
Published: Elsevier, 2018
Publish Date: 2019-06-24


By far most macromolecular crystallographic data collection and experimental phasing is nowadays carried out using synchrotron radiation. Here, we present two crystallographic datasets collected on a home-source X-ray diffractometer, which can per se be use to experimentally solve the atomic-resolution crystal structure of the Src homology 3(SH3)-like domain from the postsynaptic protein Shank3. The refined structure was described in the article “Structure of an unconventional SH3 domain from the postsynaptic density protein Shank3 at ultrahigh resolution” (Ponna et al., 2017) [1]. Crystals of the Shank3 SH3 domain were derivatized through soaking in 1 M sodium iodide prior to diffraction data collection at a wavelength of 1.54 Å. High-resolution data are reported for a native crystal to 1.01 Å and an iodide-derivatized one to 1.60 Å. The crystals suffered from several anomalies affecting experimental phasing: a high fraction (34–40%) of pseudomerohedral twinning, significant pseudotranslational symmetry (> 15%) with the operator 0.5,0,0.5, and a low solvent content. Twinning with the operator h,-k,-l is made possible by the space group P21 coupled with a unit cell β angle of 90.0°. The data can be used to repeat and optimize derivatization and phasing procedures, to understand halide interactions with protein surfaces, to promote the use of home X-ray sources for protein structure determination, as well as for educational purposes and protocol development.

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Series: Data in brief
ISSN: 2352-3409
ISSN-E: 2352-3409
ISSN-L: 2352-3409
Volume: 20
Pages: 1912 - 1916
DOI: 10.1016/j.dib.2018.09.040
Type of Publication: A1 Journal article – refereed
Field of Science: 1182 Biochemistry, cell and molecular biology
Funding: This work has been supported by grantsfrom the Emil Aaltonen Foundation and the Sigrid Jusélius Foundation (Finland). SKP has been funded through the TissueHome Joint Ph.D. Degree program between the Universities of Oulu and Ulm.
Dataset Reference: The supplementary archive contains the two crystallographic datasets, corresponding to the data discussed above and shown in Table 1 and Fig. 1. The data are in the ASCII format of the software SCALEPACK [3], and named as follows:,
Copyright information: © 2018 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (